Why don't you post your code here instead?

Instead of manually splitting up your source file, you could write a program to split up your source file and then compare the split up parts. You could also skip the part where you write out your input file into separate files and compare the split up parts in memory instead of writing them out to files and reading them back in.

So far, I get the impression that you have not really put much thought into possible approaches. Maybe you shouldn't attack the problem as a whole, but instead simplify the problem first:

• If you have two files, how do you determine their differences?
• If you have one file with two sets of routes, how can you read that file into two memory structures?
• If you have one file with more than two sets of routes, how will you determine the differences?